crossing96/oncoscreening huggingface dataset:
CDKN2A as transcriptomic marker for muscle-invasive bladder cancer risk stratification and therapy decision-making.	Deletions of the cell cycle control gene CDKN2A are described as progression markers of non-muscle invasive bladder cancer and to be associated with fibroblast growth factor 3 (FGFR3) mutations. The prognostic role of CDKN2A RNA expression in muscle invasive bladder cancer (MIBC) is under discussion. In 80 MIBC patients (m/f 60/20) who underwent radical cystectomy the expression of CDKN2A and FGFR3 was examined with qRT-PCR (test cohort). The MDA cohort (n = 57) and the TCGA cohort (n = 365) served for validation. The expression of drug target genes and TCGA molecular subtypes was correlated with CDKN2A expression. In the test cohort CDKN2A(high) patients (n = 8; 10.0%) had a significantly shorter recurrence-free (p = 0.018) and disease-specific (p = 0.006) survival compared to the rest of the cohort. A similar stratification was seen in the validation cohorts (CDKN2A(high): n = 7, 12.3%, p = 0.001; n = 46, 12.6%, p = 0.011). In the TCGA cohort these patients had a comparably low expression of drug target genes. The expression of CDKN2A significantly differed among TGCA molecular subtypes. 71.7% of CDKN2A(high) were TCGA basal squamous tumours but also show divergent molecular features compared to this group. In summary CDKN2A RNA expression-based risk stratification of MIBC allows the identification of a CDKN2A(high) poor prognosis group with low expression of drug target genes.	bladder
RETRACTED: Baicalein inhibits proliferation and migration of bladder cancer cell line T24 by down-regulation of microRNA-106.	This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been retracted at the request of the Editor-in-Chief. A panel from Figure 2A appears similar to a panel from Figure 6C of the article published by Qiu Hong Rui, Jian Bo Ma, Yu Feng Liao, Jin Hua Dai and Zhen Yu Cai in the Brazilian Journal of Medical and Biological Research 52(4) (2019) e7728 http://dx.doi.org/10.1590/1414-431X20197728. Also, panels from Figure 4F appear similar to panels from Figure 6C of the article published by the Brazilian Journal of Medical and Biological Research 52(4) (2019) e7728 and Figure 2B of the article published by Jin Zhou, Hao Li, Na Li, Xiangpan Li, Huibo Zhang, Qibin Song and Min Peng in the International Journal of Clinical and Experimental Pathology 10(8) (2017) 8211–8221 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6965428/. The journal also requested a response from the corresponding author on the post-publication comments of Dr Elisabeth Bik https://scienceintegritydigest.com/2020/02/21/the-tadpole-paper-mill/ but did not receive a response. Although this article was published earlier than the article from the Brazilian Journal of Medical and Biological Research, the Editor decided to retract this article given the concerns on the reliability of the data. Also, one of the conditions of submission of a paper for publication is that authors declare explicitly that their work is original. As such this article represents an abuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process.	bladder
Additive antitumor effect of arsenic trioxide combined with intravesical bacillus Calmette-Guerin immunotherapy against bladder cancer through blockade of the IER3/Nrf2 pathway.	BACKGROUND: As an inorganic compound used to treat various cancers and other diseases, arsenic trioxide (As(2)O(3)) has been reported to induce cellular apoptosis in certain kinds of cancers including bladder cancer. The aim of the present study was to elucidate the crucial cooperative role of As(2)O(3) and intravesical bacillus Calmette-Guerin (BCG) immunotherapy and its ability to protect against bladder cancer by targeting the IER3/Nrf2 pathway. METHOD: Initially, an orthotopic bladder cancer model was established in mice by means of intravesical instillation of the human bladder cancer cell line 5637. The expression of IL-6/IL-8 in dendritic cells (DCs) and the proportion of CD4(+) cells and ratio of CD4(+)/CD8(+) T cells were subsequently determined. RT-qPCR and Western blot assay methods were employed to determine the expressions of IER3, Nrf2, NQO1, IL-6 and IL-8. Finally, tumor cell apoptosis and the volume and weight of the in vivo tumors were evaluated in an attempt to determine the contributory role of As(2)O(3) in combination with BCG immunotherapy in treating bladder cancer. RESULTS: The additive effect of As(2)O(3) and BCG was demonstrated to promote the expressions of IL-6/IL-8 among DCs. Additionally, the proportion of CD4(+) cells, ratio of CD4(+)/CD8(+) T cells and rate of tumor cell apoptosis were all elevated, while decreased in vivo tumor volume and weight were detected. Of importance, we determined the role that ad-shNrf2 (adenoviral vectors expressing shRNA against Nrf2) played in inhibiting the effects of As(2)O(3) on bladder cancer. CONCLUSION: Taken together, the key findings of the present study provide evidence defining the effect of As(2)O(3) on inducing the inhibitory effect of BCG on the development of bladder cancer via the IER3/Nrf2 pathway, highlighting the potential of As(2)O(3) as a treatment option for bladder cancer through its enhancement of intravesical BCG.	bladder
Targeting immunotherapy for bladder cancer using anti-CD3× B7-H3 bispecific antibody.	OBJECTIVE: B7-H3 is attractive for cancer immunotherapy with B7-H3 overexpressed tumors. To explore whether B7-H3 is an effective target for patients with bladder cancer, anti-CD3× anti-B7-H3 bispecific antibodies (B7-H3Bi-Ab) was armed with activated T cells (ATC) to kill bladder cancer cells. METHODS: High expressions of B7-H3 on human bladder cancer cells were detected, including Pumc-91 and T24 cells, and their chemotherapeutic drug-resistant counterparts. ATC generated from healthy donors were stimulated with anti-CD3 monoclonal antibody and interleukin-2 (IL-2) for 13 days. The ability of ATC armed with B7-H3Bi-Ab to kill bladder cancer cells was detected by flow cytometry, LDH, Elisa, and luciferase quantitative assay. Moreover, ATC generated from bladder cancer patients was armed with B7-H3Bi-Ab to verity the cell killing by the methods as previously described. RESULTS: Compared with unarmed ATC, a significant increased cytotoxicity of B7-H3Bi-Ab-armed ATC against bladder cancer cells was discovered. The B7-H3Bi-Ab-armed ATC secreted more IFN-γ, TNF-α, and expressed high levels of activation marker CD69. Interestingly, despite the presence of immunosuppression in patients and resistance in chemotherapeutic drug-resistant cancer cell lines, B7-H3Bi-Ab-armed ATC from patients with bladder cancer still showed significant cytotoxic activity against bladder cancer cells and their chemotherapeutic drug-resistant counterparts. CONCLUSION: B7-H3 is an effective target for bladder cancer. B7-H3Bi-Ab enhances the ability of ATC to kill bladder cancer cells. B7-H3Bi-Ab-armed ATC is promisingly to provide a novel strategy for current bladder cancer therapy.	bladder
Quantitative Identification of Nonmuscle-Invasive and Muscle-Invasive Bladder Carcinomas: A Multiparametric MRI Radiomics Analysis.	BACKGROUND: Preoperative discrimination between nonmuscle-invasive bladder carcinomas (NMIBC) and the muscle-invasive ones (MIBC) is very crucial in the management of patients with bladder cancer (BC). PURPOSE: To evaluate the discriminative performance of multiparametric MRI radiomics features for precise differentiation of NMIBC from MIBC, preoperatively. STUDY TYPE: Retrospective, radiomics. POPULATION: Fifty-four patients with postoperative pathologically proven BC lesions (24 in NMIBC and 30 in MIBC groups) were included. FIELD STRENGTH/SEQUENCE: 3.0T MRI/T(2) -weighted (T(2) W) and multi-b-value diffusion-weighted (DW) sequences. ASSESSMENT: A total of 1104 radiomics features were extracted from carcinomatous regions of interest on T(2) W and DW images, and the apparent diffusion coefficient maps. Support vector machine with recursive feature elimination (SVM-RFE) and synthetic minority oversampling technique (SMOTE) were used to construct an optimal discriminative model, and its performance was evaluated and compared with that of using visual diagnoses by experts. STATISTICAL TESTS: Chi-square test and Student's t-test were applied on clinical characteristics to analyze the significant differences between patient groups. RESULTS: Of the 1104 features, an optimal subset involving 19 features was selected from T(2) W and DW sequences, which outperformed the other two subsets selected from T(2) W or DW sequence in muscle invasion discrimination. The best performance for the differentiation task was achieved by the SVM-RFE+SMOTE classifier, with averaged sensitivity, specificity, accuracy, and area under the curve of receiver operating characteristic of 92.60%, 100%, 96.30%, and 0.9857, respectively, which outperformed the diagnostic accuracy by experts. DATA CONCLUSION: The proposed radiomics approach has potential for the accurate differentiation of muscle invasion in BC, preoperatively. The optimal feature subset selected from multiparametric MR images demonstrated better performance in identifying muscle invasiveness when compared with that from T(2) W sequence or DW sequence only. LEVEL OF EVIDENCE: 3 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2019;49:1489-1498.	bladder
Second Transurethral Resection of Bladder Tumor: Is it Necessary in All T1 and/or High-Grade Tumors?	PURPOSE: To evaluate the role of second transurethral resection of bladder tumor (TURBT) in patients with T1 and/or high-grade bladder tumor regarding tumor size, multiplicity, and presence or absence of muscle in specimens of initial resection. MATERIALS AND METHODS: A total of 107 patients with either primary T1 or high-grade urothelial bladder cancer underwent second TURBT within 6 weeks after initial surgery and prior to starting intravesical immunotherapy. We assessed the incidence of residual disease and upstaging in second TURBT. RESULTS: Upstaging was noted in 11 (10.3%) patients and residual tumor was evident in 29 (27%) patients. Disease upstaging had a statistically significant association with tumor size, multifocality, and absence of muscle at initial resection in univariate analysis. Presence of residual tumor in second resection also showed significant association with tumor size and absence of muscle at initial resection but not multifocality. Multivariate logistic regression analysis revealed that absence of muscle at initial resection independently predicts disease upstaging during second TURBT (OR = 8.123, 95% CI: 1.478-44.632). Furthermore, both tumor size (OR = 13.573, 95% CI: 3.104-59.359) and absence of muscle (OR = 21.214, 95% CI: 6.062-74.244) were independent predictors of residual disease in second TURBT. CONCLUSION: We showed that second TURBT in a subset of patients with single, small T1 and/or high-grade tumor who underwent complete initial resection might be of limited value.	bladder
Influence of Transurethral Resection of Bladder Cancer on Sexual Function, Anxiety, and Depression.	The standard of care in non-muscle invasive bladder cancer consists of transurethral tumor resection. The aim of this study was to evaluate the influence of transurethral resection of bladder tumor (TURB) on the patients' self-reported depression, anxiety, sexual satisfaction, and erectile dysfunction. Psychological condition of 252 male patients who underwent TURB was prospectively evaluated. The Hospital Anxiety and Depression Scale (HADS), simplified International Index of Erectile Function (IIEF-5), and Sexual Satisfaction Questionnaires (SSQ) were administered to patients before and 10 days after tumor resection. We found that primary anxiety, depression, and erectile dysfunction were all worse in cancer patients than those in the general population, and all further worsened after tumor resection. The post-resection worsening was influenced by the operation and catheterization time, complications, and the tumor characteristics. Taxonomical analysis shows that the greatest risk of depression aggravation concerned patients who were younger, had a higher body mass index, and a medium-sized tumor. We conclude that transurethral resection of non-muscle invasive bladder cancer may adversely affect sexual function, anxiety, and depression. Patients should be informed about potential complications to prevent the abandonment of a follow-up. The findings of this study stress the role of personalized medicine pursued by a multidisciplinary medical team.	bladder
CDK4/6 Inhibitor as a Novel Therapeutic Approach for Advanced Bladder Cancer Independently of RB1 Status.	PURPOSE: Bladder cancer is a clinical and social problem due to its high incidence and recurrence rates. It frequently appears in elderly patients showing other medical comorbidities that hamper the use of standard chemotherapy. We evaluated the activity of CDK4/6 inhibitor as a new therapy for patients unfit for cisplatin (CDDP). EXPERIMENTAL DESIGN: Bladder cancer cell lines were tested for in vitro sensitivity to CDK4/6 inhibition. A novel metastatic bladder cancer mouse model was developed and used to test its in vivo activity. RESULTS: Cell lines tested were sensitive to CDK4/6 inhibition, independent on RB1 gene status. Transcriptome analyses and knockdown experiments revealed a major role for FOXM1 in this response. CDK4/6 inhibition resulted in reduced FOXM1 phosphorylation in vitro and in vivo and showed synergy with CDDP, allowing a significant tumor regression. FOXM1 exerted important oncogenic roles in bladder cancer. CONCLUSIONS: CDK4/6 inhibitors, alone or in combination, are a novel therapeutic strategy for patients with advanced bladder cancer previously classified as unfit for current treatment options.	bladder
Update of the ICUD-SIU International Consultation on Bladder Cancer 2018: urinary diversion.	"PURPOSE: To provide a comprehensive overview and update of the joint consultation of the International Consultation on Urological Diseases (ICUD) and Société Internationale d'Urologie on Bladder Cancer Urinary Diversion (UD). METHODS: A detailed analysis of the literature was conducted reporting on the different modalities of UD. For this updated publication, an exhaustive search was conducted in PubMed for recent relevant papers published between October 2013 and August 2018. Via this search, a total of 438 references were identified and 52 of them were finally eligible for analysis. An international, multidisciplinary expert committee evaluated and graded the data according to the Oxford System of Evidence-based Medicine. RESULTS: The incidence of early complications has been reported retrospectively in the range of 20-57%. Unfortunately, only a few randomized controlled studies exist within the field of UD. Consequently, almost all studies used in this report are of level 3-4 evidence including expert opinion based on ""first principles"" research. CONCLUSIONS: Complications rates overall following RC and UD are significant, and when strict reporting criteria are incorporated, they are much higher than previously published. Complications can occur up to 20 years after surgery, emphasizing the need for lifelong follow-up. Progress has been made to prevent complications implementing robotic surgery and fast track protocols. Preoperative patient information, patient selection, surgical techniques, and careful postoperative follow-up are the cornerstones to achieve good results."	bladder
UPK1B promotes the invasion and metastasis of bladder cancer via regulating the Wnt/β-catenin pathway.	OBJECTIVE: The aim of this study was to investigate the expression of UPK1B in bladder cancer (BCa), and to further explore the correlation between UPK1B expression and pathological parameters as well as the prognosis of BCa. PATIENTS AND METHODS: Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the expression of UPK1B in 92 pairs of BCa tissues and adjacent normal tissues. The relationship between UPK1B expression and pathological features as well as the prognosis of BCa patients was further analyzed. For in vitro experiments, the mRNA expression level of UPK1B in BCa cell lines (EJ and T-24) was detected by qRT-PCR. In addition, knockdown of UPK1B in BCa cells was constructed using small interfering RNA. Effects of UPK1B knockdown on biological functions of BCa cells were analyzed by Cell Counting Kit-8 (CCK-8), colony formation assay and transwell assay, respectively. Furthermore, the underlying mechanism of UPK1B in regulating BCa was evaluated by Western blot and qRT-PCR, respectively. RESULTS: The expression of UPK1B in BCa tissues was remarkably higher than that of adjacent normal tissues (p<0.05). Compared with BCa patients with lower UPK1B expression, those with higher UPK1B expression exhibited higher tumor stage, lymph node metastasis and distant metastasis. In vitro experiments indicated that cell proliferation, invasion and metastasis were remarkably decreased in cells transfected with si-UPK1B when compared with those transfected with negative controls. Western blot showed that the expression of key proteins in the Wnt/β-catenin signaling pathway in cells transfected with si-UPK1B was significantly down-regulated compared with those transfected with negative controls, including β-catenin, c-myc and cyclinD1. In addition, rescue experiments found that UPK1B was regulated by β-catenin. CONCLUSIONS: UPK1B is upregulated in BCa, and is significantly correlated with tumor stage, lymph node metastasis, distant metastasis and poor prognosis of BCa. Moreover, UPK1B promotes the proliferation, invasion and migration of BCa via regulating the Wnt/β-catenin signaling pathway.	bladder
TSNAdb: A Database for Tumor-specific Neoantigens from Immunogenomics Data Analysis.	Tumor-specific neoantigens have attracted much attention since they can be used as biomarkers to predict therapeutic effects of immune checkpoint blockade therapy and as potential targets for cancer immunotherapy. In this study, we developed a comprehensive tumor-specific neoantigen database (TSNAdb v1.0), based on pan-cancer immunogenomic analyses of somatic mutation data and human leukocyte antigen (HLA) allele information for 16 tumor types with 7748 tumor samples from The Cancer Genome Atlas (TCGA) and The Cancer Immunome Atlas (TCIA). We predicted binding affinities between mutant/wild-type peptides and HLA class I molecules by NetMHCpan v2.8/v4.0, and presented detailed information of 3,707,562/1,146,961 potential neoantigens generated by somatic mutations of all tumor samples. Moreover, we employed recurrent mutations in combination with highly frequent HLA alleles to predict potential shared neoantigens across tumor patients, which would facilitate the discovery of putative targets for neoantigen-based cancer immunotherapy. TSNAdb is freely available at http://biopharm.zju.edu.cn/tsnadb.	bladder
Ileus and small bowel obstruction after radical cystectomy for bladder cancer: Analysis from the Nationwide Inpatient Sample.	PURPOSE: To investigate prevalence and predictors of postoperative small bowel obstruction (SBO) and ileus in a large cohort of bladder cancer (BCa) patients treated with radical cystectomy (RC). METHODS: All patients within the Nationwide Inpatient Sample who underwent RC for BCa between 2006 and 2012 were identified. First, prevalence of SBO and ileus was analyzed. Second, predictors of these bowel-related complications were identified using multivariable regression analyses. Third, the association between SBO, ileus, and length of stay was evaluated using logistic regression models adjusted for clustering. Prolonged length of stay was defined as hospital stay above mean stay of the population (>10 days). Fourth, the effect of SBO and ileus on mean inpatient cost of healthcare was examined. RESULTS: Of overall 41,498 patients, 1071 (2.6%) experienced SBO, and 11,155 (26.9%) experienced ileus. Predictors of ileus included age, male gender, black race, hospital characteristics, anemia, chronic pulmonary disease, drug abuse, hypothyroidism, fluid and electrolyte disorders, and neurological disorders (all p < 0.05) Predictors of SBO included male gender, Asian/Pacific islander race, hospital characteristics, congestive heart failure, fluid and electrolyte disorders, and psychosis (all p < 0.05). . Postoperative SBO (odds ratio (OR) 19.587; 95% confidence interval (CI):15.869-24.167) and ileus (OR 5.646; 95% CI:5.336-5.974) were associated with prolonged length of stay (all p < 0.001).Median cost of hospital stay was $56.315 for patients who developed SBO, $32,472 for patients who developed ileus, and $24,600 for patients after cystectomy without ileus or SBO. CONCLUSIONS: Significant prevalence of bowel-related complications in patients after RC was observed. These complications are strongly associated with prolonged length of stay and higher healthcare cost. Increasing awareness of SBO and ileus, identification of patients at risk prior to surgery, and implementation of protective strategies are strongly indicated in cystectomy patients.	bladder
Mycotic Aortic Aneurysm and Infected Aortic Graft After Intravesical Bacillus Calmette-Guérin Treatment for Bladder Cancer.	Although intravesical therapy with bacillus Calmette-Guérin (BCG) has proven its efficiency in the treatment of early-stage bladder cancer, infectious complications can occur and mycotic aneurysms represent a rare but life-threatening complication. Here, we report the case of an aortic graft infection in a patient with abdominal aortic aneurysm who received BCG instillations for the treatment of bladder cancer. Based on the current knowledge on this rare vascular complication, we discuss factors that may have contributed to its occurrence and review issues to optimize its management and early detection.	bladder
[ypT0N0 after neoadjuvant chemotherapy and cystectomy for muscle-invasive bladder cancer: Incidence and prognosis. A review from the Bladder group of the French Committee of Oncology].	"INTRODUCTION: Neoadjuvant chemotherapy (NAC) is recommended for localized muscle-invasive bladder cancer when patients are fit for cisplatin-based chemotherapy. A pathological complete response can be observed, corresponding to ypT0N0 stage on the radical cystectomy specimen. This review discusses the incidence, prognosis and potential therapeutic impact of complete response on pathological specimen in NAC treated patients. METHODS: A comprehensive review of the literature was conducted using Medline database, with no time frame. The articles were selected using the following keywords association: ""Bladder cancer"" (Mesh) AND ""Neoadjuvant chemotherapy"" (Mesh) AND ""pT0"" (Mesh). RESULTS: After NAC, ypT0N0 rates vary from 9 to 46% among the series, reported rates that are higher compared to those of pT0 without NAC administration. The incidence depends on the chemotherapy regimen (maximal local effect with cisplatin-based chemotherapy) and the pathological type of the disease (presence of variant histologies). Molecular analyses of bladder cancer could probably help in the near future to identify and predict NAC responders. Pathological complete response is associated with a favorable prognosis in terms of recurrence-free and overall survival. Nevertheless, disease recurrences are still observed in 10-15% of cases, which underlies the importance of local treatment and close follow-up even in these patients. CONCLUSION: ypT0N0 rate is approximately 25% after NAC, that is 4.3 higher than after bladder resection alone. The prognosis is better than that with residual tumor on specimen and is comparable to that of pT0 without NAC administration."	bladder